Saturday, October 29, 2011

'Genetic biopsy' of human eggs might help pick the best for IVF

Given the stakes of in vitro fertilization, prospective parents and their doctors need the best information they can get about the eggs they will extract, attempt to fertilize, and implant. New research at Brown University and Women & Infants Hospital of Rhode Island has found a way to see which genes each egg cell is expressing without harming it. As researchers learn more about how those genes affect embryo development, the new technique could ultimately give parents and doctors a preview of which eggs are likely to make the most viable embryos.

In the research, now in press in the Journal of Biological Chemistry, the team of physicians and biologists were able to sequence the transcribed genetic material, or mRNA, in egg cells and, in a scientific first, in smaller structures pinched off from them called "polar bodies." By comparing the gene expression sequences in polar bodies and their host eggs, the researchers were able to determine that the polar bodies offer a faithful reflection of the eggs' genetic activity.

"We can now consider the a natural cytoplasmic biopsy," said study co-author Sandra Carson, professor obstetrics and gynecology at the Warren Alpert Medical School of Brown University and director of the Center for Reproduction and Infertility at Women & Infants Hospital.

Polar bodies are where egg cells dispense with the second copies of chromosomes that, as sex cells, they don't need. But the polar bodies also capture a microcosm of the egg's mRNA, the genetic material produced when genes have been transcribed and a cell is set to make proteins based on those genetic instructions.

Pairs of genes

Last year the team became the first to find mRNA in human polar bodies. Now they have transcribed it in 22 pairs of human eggs and their polar bodies, and confirmed that what is in the polar bodies is a good proxy for what is in the eggs.

Given how little mRNA is present in polar bodies, the task was not easy, said Gary Wessel, professor of biology, but through a combination of clever amplification and analysis techniques by lead author and graduate student Adrian Reich and second author Peter Klatsky, the team got it done.

"There's no reason this should have worked, just because there was so little material," Wessel said. "Single-cell sequencing is very challenging."

To hedge their bets the team analyzed most of their samples in two pools of 10 cells each, for instance comparing the mRNA in 10 eggs with the mRNA in the 10 related polar bodies. But to their pleasant surprise, they were also able to sequence two individual eggs and their polar bodies directly.

What they found is that more than 14,000 genes can be expressed in the eggs. Of those, more than 90 percent of the genes detected in the polar bodies were also detected in the eggs and of the 700 most abundant genes found in the polar bodies, 460 were also among the most abundant in the eggs.

Toward clinical use

"It seems that the polar body does reflect what is in the egg," Carson said. "Because the egg is the major driver of the first three days of human embryo development, what we find in the polar body may give us a clue into what is happening during that time."

But Carson and Wessel acknowledged that more research will be required to create a clinically useful tool.

Finding which genes affect embryo viability is the next major step. With the new knowledge and techniques developed in their study, the researchers said, scientists could analyze the mRNA from polar bodies of eggs that are fertilized and track the progress of the resulting embryos. Once the key genes are known, they could create fast assays to look for those in polar bodies so that clinicians and patients could pick the best eggs. A sufficiently developed technology could also be used for choosing which to bank for later use.

"We don't quite have the answer of what those messages are doing exactly or necessarily the purpose of them in the cell function, but that's to come," Carson said. "Now we have the words, but not the sentences."

Provided by Brown University (news : web)

Researchers watch amyloid plaques form

Researchers at the University of Toronto Scarborough (UTSC) and Osaka University applied a new approach to take a close look at amyloid plaque formation, a process that plays important roles in Alzheimer's disease. The technique would greatly aid the development and screening for novel therapeutics that can manipulate the formation of the toxic amyloid aggregates.

Anthony Veloso, Prof. Kagan Kerman's PhD student in Chemistry, used a laser to trap amyloid-beta peptides and examined them under a fluorescence microscope as they aggregate, giving them an exceptionally detailed view of the process. The work appears on the cover of the current issue of Analyst, a journal of the Royal Society of Chemistry.

"This technique could accelerate the process. It gives us a new way to examine the early phase of , when the most of are formed," says Prof. Kerman, a faculty with the Department of Physical and Environmental Sciences at UTSC and the corresponding author on the paper.

Amyloid plaques are protein deposits that form around neurons and interfere with their function. The major constituent of these deposits are amyloid-beta, a peptide that clumps together to form harmful plaques in Alzheimer's patients, but is otherwise harmless in normal individuals.

To get a look at the early stages of the process, the Canadian researchers and their Japanese collaborators used a technique called optical trapping. A laser is focused into a very thin beam and aimed at solution containing amyloid-beta particles. The beam creates a small magnetic field, which attracts and holds the particles in place. Amyloid aggregates stained by a dye then glows under the , and the image can be captured by .

By using this technique, A. Veloso and Prof. Kerman hope to explore how the aggregates are formed, and to eventually discover the role of amyloid aggregates in Alzheimer's disease. Utilizing the versatility of this technique, Prof. Kerman's research team can extend their studies to understand aggregate formation in other neurodegenerative diseases.

The technique will also become a novel strategy to test therapeutic compounds that could halt the formation of plaques. Prof. Kerman and A. Veloso are working towards the automation of the technique, allowing for many compounds to be tested efficiently.

Provided by University of Toronto Scarborough

New membrane lipid measuring technique may help fight disease

Could controlling cell-membrane fat play a key role in turning off disease?

Researchers at the University of Illinois at Chicago think so, and a biosensor they've created that measures levels may open up new pathways to disease treatment.

Wonhwa Cho, distinguished professor of chemistry, and his coworkers engineered a way to modify proteins to fluoresce and act as sensors for .

Their findings are reported in Nature Chemistry, online on Oct. 9.

"Lipid molecules on cell membranes can act as switches that turn on or off protein-protein interactions affecting all cellular processes, including those associated with disease," says Cho. "While the exact mechanism is still unknown, our hypothesis is that lipid molecules serve sort of like a sliding switch."

Cho said once lipid concentrations reach a certain threshold, they trigger reactions, including disease-fighting immune responses. Quantifying concentration in a living cell and studying its location in real time can provide a powerful tool for understanding and developing new ways to combat a range of maladies from inflammation, cancer and diabetes to .

"It's not just the presence of lipid, but the number of lipid molecules that are important for turning on and off biological activity," said Cho.

While visualizing with fluorescent proteins isn't new, Cho's technique allows quantification by using a hybrid that fluoresces only when it binds specific lipids. His lab worked with a lipid known as PIP2 -- an important fat molecule involved in many . Cho's sensor binds to PIP2 and gives a clear signal that can be quantified through a fluorescent microscope.

The result is the first successful quantification of membrane lipids in a living cell in real time.

"We had to engineer the protein in such a way to make it very stable, behave well, and specifically recognizes a particular lipid," Cho said. He has been working on the technique for about a decade, overcoming technical obstacles only about three years ago.

Cho hopes now to create a tool kit of biosensors to quantify most, if not all lipids.

"We'd like to be able to measure multiple lipids, simultaneously," he said. "It would give us a snapshot of all the processes being regulated by the different lipids inside a cell."

Provided by University of Illinois at Chicago (news : web)

Perspective article examines conductivity at the LaAlO3 and SrTiO3 (001) interface

Complex oxides have the potential to inject new functionalities into technologies that require semiconductors.  The correlated behavior of itinerant electrons in these materials sets complex oxides apart from traditional semiconductors such as Si and GaAs. Potential applications abound, but the fundamental properties of these materials, particularly when combined to make interfaces, must be understood.  In an invited Perspective article in Surface Science, Dr. Scott Chambers of PNNL examines conductivity at the interface of polar and nonpolar complex oxides from outside the reigning paradigm and considers how unintentional dopants and defects, resulting from interfacial mixing, might affect the electronic properties.

The common paradigm used to explain the observation of at interfaces of materials such as lanthanum aluminate and strontium titanate is that electrons move across the interface to alleviate the so-called polar catastrophe created by polar/nonpolar interface creation.  Based on a number of different experimental results, Chambers argues that this simple paradigm is inadequate to explain observed conductivity.

"Intermixing occurs, and the resulting cation rearrangement cannot be ignored," said Chambers, a Fellow of the AVS and the American Association for the Advancement of Science. "Moreover, defects and dopants appear to play a role in facilitating, if not enabling conductivity."

Providing insights into the fundamental relationships between composition/structure, and the resulting electronic, magnetic, and surface chemical properties of complex could enable these materials to have an impact on next-generation electronics, chemical sensors, and photocatalysts. These advances could include more energy-efficient field effect transistors and photocatalysts that use visible light from the sun.

Chambers and his colleagues around the world are continuing to make strides in understanding the complex relationships between atom distributions near the interface and conductivity. One upshot is that significantly more insight into the growth process is necessary to characterize and ultimately control defect creation during heterojunction formation.

"Then and only then can structures suspected of facilitating conductivity be changed to see if doing so actually reduces or eliminates conductivity," said Chambers.

More information: Chambers SA. 2011. "Understanding the Mechanism of Conductivity at the LaAlO3 and SrTiO3 (001) Interface." Surface Science 605:1133-1140.

Provided by Pacific Northwest National Laboratory (news : web)

Building better catalysts: Chemists find new way to design important molecules

University of Utah chemists developed a method to design and test new catalysts, which are substances that speed chemical reactions and are crucial for producing energy, chemicals and industrial products. By using the new method, the chemists also made a discovery that will make it easier to design future catalysts.

The discovery: the sizes and electronic properties of catalysts interact to affect how well a performs, and are not independent factors as was thought previously. Chemistry Professor Matt Sigman and doctoral student Kaid Harper, report their findings in the Friday, Sept. 30, 2011, issue of the journal Science.

“It opens our eyes to how to design new catalysts that we wouldn’t necessarily think about designing, for a broad range of reactions,” Sigman says. “We’re pretty excited.”

Sigman believes the new technique for designing and testing catalysts “is going to be picked up pretty fast,” first by academic and then by industrial , who “will see it’s a simple way to rapidly design better catalysts.”

The new study was funded by the National Science Foundation.

‘Catalysts Make the World Go ‘Round’

Catalysts speed chemical reactions without being consumed by those reactions. Their importance to society and the economy is tough to overstate. Products made with catalysts include medicines, fuels, foods and fertilizers.

Ninety percent of U.S. chemical manufacturing processes involve catalysts, which also are used to make more than one-fifth of all industrial products. Those processes consume much energy, so making catalytic reactions more efficient would both save energy and reduce emissions of climate-warming carbon dioxide gas.

“Catalysts make the world go ‘round,” says Sigman. “Catalysts are how we make molecules more efficiently and, more important, make molecules that can’t be made using any other method.”

The Utah researchers developed a new method for rapidly identifying and designing what are known as “asymmetric catalysts,” which are catalyst molecules that are considered either left-handed or right-handed because they are physically asymmetrical. In chemistry, this property of handedness is known as chirality.

Chemists want new asymmetric catalysts because they impart handedness or chirality to the molecules they are used to make. For example, when a left-handed or right-handed catalyst is used to speed a chemical reaction, the chemical that results from that reaction can be either left-handed or right-handed.

“Handedness is an essential component of a drug’s effectiveness,” Sigman says.

Drugs generally work by latching onto proteins involved in a disease-causing process. The drug is like a key that fits into a protein lock, and chirality “is the direction the key goes” to fit properly and open the lock, says Sigman.

“However, developing asymmetric catalysts [to produce asymmetric drug molecules] can be a time-consuming and sometimes unsuccessful undertaking” because it usually is done by trial and error, he adds.

Sigman says the new study “is a step toward developing faster methods to identify optimal catalysts and insight into how to design them.”

A Mathematical Approach to Catalyst Design

Harper and Sigman combined principles of data analysis with principles of catalyst design to create a “library” of nine related catalysts that they hypothesized would effectively catalyze a given reaction – one that could be useful for making new pharmaceuticals. Essentially, they used math to find the optimal size and electronic properties of the candidate catalysts.

Then the chemists tested the nine catalysts – known as “quinoline proline ligands” – to determine how well their degree of handedness would be passed on to the reaction products the catalysts were used to produce.

Sigman and Harper depicted results of the reactions using the different catalysts as a three-dimensional mathematical surface that bulges upward. The highest part of the bulge represents those among the nine catalysts that had the greatest degree of handedness.

This technique was used – and can be used in the future – to identify the optimal catalysts among a number of candidates. But it also revealed the unexpected link between the size and of catalysts in determining their effectiveness in speeding reactions.

“This study shows quantitatively that the two factors are related,” and knowing that will make it easier to design many future catalysts, Sigman says.

Provided by University of Utah (news : web)